用户名: 密码: 验证码:
Thermodynamic Proxies to Compensate for Biases in Drug Discovery Methods
详细信息    查看全文
  • 作者:Sean Ekins ; Nadia K. Litterman ; Christopher A. Lipinski…
  • 关键词:enthalpy ; entropy ; high ; throughput screening ; structure based drug design ; tuberculosis
  • 刊名:Pharmaceutical Research
  • 出版年:2016
  • 出版时间:January 2016
  • 年:2016
  • 卷:33
  • 期:1
  • 页码:194-205
  • 全文大小:1,314 KB
  • 参考文献:1.Macarron R, Banks MN, Bojanic D, Burns DJ, Cirovic DA, Garyantes T, et al. Impact of high-throughput screening in biomedical research. Nat Rev Drug Discov. 2011;10(3):188–95.PubMed CrossRef
    2.Ananthan S, Faaleolea ER, Goldman RC, Hobrath JV, Kwong CD, Laughon BE, et al. High-throughput screening for inhibitors of Mycobacterium tuberculosis H37Rv. Tuberculosis. 2009;89:334–53.PubMed PubMedCentral CrossRef
    3.Inglese J, Shamu CE, Guy RK. Reporting data from high-throughput screening of small-molecule libraries. Nat Chem Biol. 2007;3(8):438–41.PubMed CrossRef
    4.Inglese J, Dranchak P, Moran JJ, Jang SW, Srinivasan R, Santiago Y, et al. Genome editing-enabled HTS assays expand drug target pathways for Charcot-Marie-tooth disease. ACS Chem Biol. 2014;9(11):2594–602.PubMed PubMedCentral CrossRef
    5.Jang SW, Lopez-Anido C, Macarthur R, Svaren J, Inglese J. Identification of drug modulators targeting gene-dosage disease CMT1A. ACS Chem Biol. 2012;7(7):1205–13.
    6.Zheng W, Padia J, Urban DJ, Jadhav A, Goker-Alpan O, Simeonov A, et al. Three classes of glucocerebrosidase inhibitors identified by quantitative high-throughput screening are chaperone leads for Gaucher disease. Proc Natl Acad Sci U S A. 2007;104(32):13192–7.PubMed PubMedCentral CrossRef
    7.Cain R, Narramore S, McPhillie M, Simmons K, Fishwick CW. Applications of structure-based design to antibacterial drug discovery. Bioorg Chem. 2014;55:69–76.PubMed CrossRef
    8.Lounnas V, Ritschel T, Kelder J, McGuire R, Bywater RP, Foloppe N. Current progress in structure-based rational drug design marks a new mindset in drug discovery. Comput Struct Biotechnol J. 2013;5:e201302011.PubMed PubMedCentral CrossRef
    9.Kalyaanamoorthy S, Chen YP. Structure-based drug design to augment hit discovery. Drug Discov Today. 2011;16(17–18):831–9.PubMed CrossRef
    10.Hunter WN. Structure-based ligand design and the promise held for antiprotozoan drug discovery. J Biol Chem. 2009;284(18):11749–53.PubMed PubMedCentral CrossRef
    11.Cohen NC. Structure-based drug design and the discovery of aliskiren (Tekturna): perseverance and creativity to overcome a R&D pipeline challenge. Chem Biol Drug Des. 2007;70(6):557–65.PubMed CrossRef
    12.Brigo A, Mustata GI, Briggs JM, Moro S. Discovery of HIV-1 integrase inhibitors through a novel combination of ligand and structure-based drug design. Med Chem. 2005;1(3):263–75.PubMed CrossRef
    13.Abdulla MH, Ruelas DS, Wolff B, Snedecor J, Lim KC, Xu F, et al. Drug discovery for schistosomiasis: hit and lead compounds identified in a library of known drugs by medium-throughput phenotypic screening. PLoS Negl Trop Dis. 2009;3(7):e478.PubMed PubMedCentral CrossRef
    14.Ballell L, Bates RH, Young RJ, Alvarez-Gomez D, Alvarez-Ruiz E, Barroso V, et al. Fueling open-source drug discovery: 177 small-molecule leads against tuberculosis. Chem Med Chem. 2013;8:313–21.PubMed PubMedCentral CrossRef
    15.Christophe T, Jackson M, Jeon HK, Fenistein D, Contreras-Dominguez M, Kim J, et al. High content screening identifies decaprenyl-phosphoribose 2’ epimerase as a target for intracellular antimycobacterial inhibitors. PLoS Pathog. 2009;5(10):e1000645.PubMed PubMedCentral CrossRef
    16.Murray CW, Blundell TL. Structural biology in fragment-based drug design. Curr Opin Struct Biol. 2010;20(4):497–507.PubMed CrossRef
    17.Klebe G. Applying thermodynamic profiling in lead finding and optimization. Nat Rev Drug Discov. 2015;14(2):95–110.
    18.Klebe G. The use of thermodynamic and kinetic data in drug discovery: decisive insight or increasing the puzzlement? Chem Med Chem. 2015;10(2):229–31.PubMed CrossRef
    19.Lafont V, Armstrong AA, Ohtaka H, Kiso Y, Mario Amzel L, Freire E. Compensating enthalpic and entropic changes hinder binding affinity optimization. Chem Biol Drug Des. 2007;69(6):413–22.PubMed CrossRef
    20.Ferenczy GG, Keseru GM. Thermodynamics guided lead discovery and optimization. Drug Discov Today. 2010;15(21–22):919–32.PubMed CrossRef
    21.Freire E. Thermodynamics in drug design, high affinity and selectivity, The chemical theatre of biological systems. Bozen: Beilstein -Institut; 2004.
    22.Freire E. A thermodynamic approach to the affinity optimization of drug candidates. Chem Biol Drug Des. 2009;74(5):468–72.PubMed PubMedCentral CrossRef
    23.Freire E. Do enthalpy and entropy distinguish first in class from best in class? Drug Discov Today. 2008;13(19–20):869–74.PubMed PubMedCentral CrossRef
    24.King NM, Prabu-Jeyabalan M, Bandaranayake RM, Nalam MN, Nalivaika EA, Ozen A, et al. Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease. ACS Chem Biol. 2012;7(9):1536–46.PubMed PubMedCentral CrossRef
    25.Chodera JD, Mobley DL. Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annu Rev Biophys. 2013;42:121–42.PubMed PubMedCentral CrossRef
    26.Tarcsay A, Keseru GM. Is there a link between selectivity and binding thermodynamics profiles? Drug Discov Today. 2015;20(1):86–94.PubMed CrossRef
    27.Koppisetty CA, Frank M, Kemp GJ, Nyholm PG. Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines. J Chem Inf Model. 2013;53(10):2559–70.PubMed CrossRef
    28.Whitesides GM, Krishnamurthy VM. Designing ligands to bind proteins. Q Rev Biophys. 2005;38(4):385–95.PubMed PubMedCentral CrossRef
    29.Ekins S, Olechno J, Williams AJ. Dispensing processes impact apparent biological activity as determined by computational and statistical analyses. PLoS ONE. 2013;8(5):e62325.PubMed PubMedCentral CrossRef
    30.Harris D, Olechno J, Datwani S, Ellson R. Gradient, contact-free volume transfers minimize compound loss in dose–response experiments. J Biomol Screen. 2010;15(1):86–94.PubMed CrossRef
    31.Wingfield J. Impact of acoustic dispensing on data quality in HTS and hit confirmation. In. Drug Discovery 2012. Manchester, UK; 2012.
    32.Davis BJ, Erlanson DA. Learning from our mistakes: the ‘unknown knowns’ in fragment screening. Bioorg Med Chem Lett. 2013;23(10):2844–52.PubMed CrossRef
    33.Metz JT, Huth JR, Hajduk PJ. Enhancement of chemical rules for predicting compound reactivity towards protein thiol groups. J Comput Aided Mol Des. 2007;21(1–3):139–44.PubMed CrossRef
    34.Bruns RF, Watson IA. Rules for identifying potentially reactive or promiscuous compounds. J Med Chem. 2012;55(22):9763–72.PubMed CrossRef
    35.Baell JB, Holloway GA. New substructure filters for removal of Pan Assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem. 2010;53:2719–40.PubMed CrossRef
    36.Baell J, Walters MA. Chemistry: chemical con artists foil drug discovery. Nature. 2014;513(7519):481–3.PubMed CrossRef
    37.Brown CS, Lee MS, Leung DW, Wang T, Xu W, Luthra P, et al. In silico derived small molecules bind the filovirus VP35 protein and inhibit its polymerase cofactor activity. J Mol Biol. 2014;426(10):2045–58.PubMed PubMedCentral CrossRef
    38.Pauli I, dos Santos RN, Rostirolla DC, Martinelli LK, Ducati RG, Timmers LF, et al. Discovery of new inhibitors of Mycobacterium tuberculosis InhA enzyme using virtual screening and a 3D-pharmacophore-based approach. J Chem Inf Model. 2013;53(9):2390–401.PubMed CrossRef
    39.Lill MA, Dobler M, Vedani A. Prediction of small-molecule binding to cytochrome P450 3A4: flexible docking combined with multidimensional QSAR. Chem Med Chem. 2006;6:73–81.CrossRef
    40.Meanwell NA. Improving drug candidates by design: a focus on physicochemical properties as a means of improving compound disposition and safety. Chem Res Toxicol. 2011;24(9):1420–56.PubMed CrossRef
    41.Shultz MD. Setting expectations in molecular optimizations: strengths and limitations of commonly used composite parameters. Bioorg Med Chem Lett. 2013;23(21):5980–91.PubMed CrossRef
    42.Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 1997;23:3–25.CrossRef
    43.Walters WP, Ajay Murcko MA. Recognizing molecules with drug-like properties. Curr Opin Chem Biol. 1999;3(4):384–7.PubMed CrossRef
    44.Bembenek SD, Tounge BA, Reynolds CH. Ligand efficiency and fragment-based drug discovery. Drug Discov Today. 2009;14(5–6):278–83.PubMed CrossRef
    45.Reynolds CH, Tounge BA, Bembenek SD. Ligand binding efficiency: trends, physical basis, and implications. J Med Chem. 2008;51(8):2432–8.PubMed CrossRef
    46.Wunberg T, Hendrix M, Hillisch A, Lobell M, Meier H, Schmeck C, et al. Improving the hit-to-lead process: data-driven assessment of drug-like and lead-like screening hits. Drug Discov Today. 2006;11(3–4):175–80.PubMed CrossRef
    47.Kenny PW, Leitao A, Montanari CA. Ligand efficiency metrics considered harmful. J Comput Aided Mol Des. 2014;28(7):699–710.PubMed CrossRef
    48.Tang YT, Marshall GR. PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements. J Chem Inf Model. 2011;51(2):214–28.PubMed PubMedCentral CrossRef
    49.Metz JT, Johnson EF, Soni NB, Merta PJ, Kifle L, Hajduk PJ. Navigating the kinome. Nat Chem Biol. 2011;7(4):200–2.PubMed CrossRef
    50.Drewry DH, Willson TM, Zuercher WJ. Seeding collaborations to advance kinase science with the GSK published kinase inhibitor set (PKIS). Curr Top Med Chem. 2014;14(3):340–2.PubMed PubMedCentral CrossRef
    51.Strachan RT, Ferrara G, Roth BL. Screening the receptorome: an efficient approach for drug discovery and target validation. Drug Discov Today. 2006;11(15–16):708–16.PubMed CrossRef
    52.Jensen NH, Roth BL. Massively parallel screening of the receptorome. Comb Chem High Throughput Screen. 2008;11(6):420–6.PubMed CrossRef
    53.Ekins S, Freundlich JS, Hobrath JV, White EL, Reynolds RC. Combining computational methods for hit to lead optimization in mycobacterium tuberculosis drug discovery. Pharm Res. 2014;31:414–35.
    54.Reynolds RC, Ananthan S, Faaleolea E, Hobrath JV, Kwong CD, Maddox C, et al. High throughput screening of a library based on kinase inhibitor scaffolds against Mycobacterium tuberculosis H37Rv. Tuberculosis. 2012;92:72–83.PubMed PubMedCentral CrossRef
    55.Maddry JA, Ananthan S, Goldman RC, Hobrath JV, Kwong CD, Maddox C, et al. Antituberculosis activity of the molecular libraries screening center network library. Tuberculosis. 2009;89:354–63.PubMed PubMedCentral CrossRef
    56.Clark AM, Dole K, Coulon-Spector A, McNutt A, Grass G, Freundlich JS, Reynolds RC, Ekins S. Open source bayesian models: I. Application to ADME/Tox and drug discovery datasets. J Chem Inf Model. 2015;55:1231–45.
    57.Davis MI, Hunt JP, Herrgard S, Ciceri P, Wodicka LM, Pallares G, et al. Comprehensive analysis of kinase inhibitor selectivity. Nat Biotechnol. 2011;29(11):1046–51.PubMed CrossRef
    58.Ekins S, Freundlich JS, Hobrath JV, Lucile White E, Reynolds RC. Combining computational methods for hit to lead optimization in Mycobacterium tuberculosis drug discovery. Pharm Res. 2014;31(2):414–35.PubMed PubMedCentral CrossRef
    59.Swinney DC, Anthony J. How were new medicines discovered? Nat Rev. 2011;10(7):507–19.
    60.Ekins S, Bradford J, Dole K, Spektor A, Gregory K, Blondeau D, et al. A collaborative database and computational models for tuberculosis drug discovery. Mol BioSystems. 2010;6:840–51.CrossRef
    61.Li R, Stafford JA. Kinase inhibitor drugs. Hoboken: Wiley; 2009.CrossRef
    62.Gilli P, Ferretti V, Gilli G, Borea PA. Enthalpy-entropy compensation in drug receptor binding. J Phys Chem. 1994;98:1515–8.CrossRef
    63.Ichihara O, Shimada Y, Yoshidome D. The importance of hydration thermodynamics in fragment-to-lead optimization. Chem Med Chem. 2014;9(12):2708–17.PubMed CrossRef
    64.Guo H. A simple algorithm for fitting a Gaussian function. IEEE Signal Process Mag. 2011;28:134–7.CrossRef
    65.Luque I, Freire E. Structural parameterization of the binding enthalpy of small ligands. Proteins. 2002;49(2):181–90.PubMed CrossRef
    66.Brooijmans N, Sharp KA, Kuntz ID. Stability of macromolecular complexes. Proteins. 2002;48(4):645–53.PubMed CrossRef
    67.Papadatos G, Overington JP. The ChEMBL database: a taster for medicinal chemists. Future Med Chem. 2014;6(4):361–4.PubMed CrossRef
    68.Tang J, Szwajda A, Shakyawar S, Xu T, Hintsanen P, Wennerberg K, et al. Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis. J Chem Inf Model. 2014;54(3):735–43.PubMed CrossRef
    69.Ekins S, Honeycutt JD, Metz JT. Evolving molecules using multi-objective optimization: applying to ADME. Drug Discov Today. 2010;15:451–60.PubMed CrossRef
    70.Lowe D. The palbociclib saga: or why we need a lot of drug companies. Available from: http://​pipeline.​corante.​com/​archives/​2014/​08/​22/​the_​palbociclib_​saga_​or_​why_​we_​need_​a_​lot_​of_​drug_​companies.​php .
  • 作者单位:Sean Ekins (1) (2)
    Nadia K. Litterman (1)
    Christopher A. Lipinski (3)
    Barry A. Bunin (1)

    1. Collaborative Drug Discovery, Inc., 1633 Bayshore Highway Suite 342, Burlingame, California, 94010, USA
    2. Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay Varina, North Carolina, 27526, USA
    3. 10 Connshire Drive, Waterford, Connecticut, 06385-4122, USA
  • 刊物类别:Biomedical and Life Sciences
  • 刊物主题:Biomedicine
    Pharmacology and Toxicology
    Pharmacy
    Biochemistry
    Medical Law
    Biomedical Engineering
  • 出版者:Springer Netherlands
  • ISSN:1573-904X
文摘
Purpose We propose a framework with simple proxies to dissect the relative energy contributions responsible for standard drug discovery binding activity.

© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号

地址:北京市海淀区学院路29号 邮编:100083

电话:办公室:(+86 10)66554848;文献借阅、咨询服务、科技查新:66554700